Systems biology of organellar carbon metabolism in Eucalyptus xylogenesis

Abstract

Trees play a pivotal role in the global carbon cycle through the fixation and storage of carbon as polysaccharide and phenolic biopolymers in the secondary cell walls of xylem fibre cells (wood). Driven by the need to mitigate climate change, the utilization of wood as a source of renewable lignocellulosic biomass is undergoing a technological renaissance. Fundamental research in understanding and modelling xylogenesis as a developmental program remains crucial, as most carbon in living biomass is present in the secondary growth tissues of terrestrial plants. Although systems biology approaches in poplar, Eucalyptus and Arabidopsis have made massive strides in unravelling the complex genetic regulation underpinning xylogenesis, we know little of how the genome-bearing organelles of the cell, the plastids, and mitochondria, are integrated into the system. As the location of many carbon metabolic pathways in the cell, plastids and mitochondria play a crucial role in carbon allocation during wood formation. Despite this, plastid and mitochondrial biology have largely been ignored in the study of xylogenesis, and the vast majority of plant organellar research is focused on photosynthetic tissues. The work presented in this thesis aimed to provide a basis for understanding the role of plastid and mitochondrial biology during xylogenesis, using Eucalyptus as a model. This was achieved through three research objectives: (i.) The analysis of coregulated expression modules of nuclear-encoded plastid and mitochondrial-targeted genes generated from 156 xylem transcriptomes from a Eucalyptus grandis × E. urophylla F2 interspecific backcross population; (ii.) The assembly and annotation of the plastid and mitochondrial genomes of E. grandis, along with analysis of intergenomic DNA transfers and their expression; and (iii.) Comprehensive analysis of the transcriptomes of E. grandis plastids and mitochondria using total RNA, polyA-selected RNA, and small RNA sequencing data to understand the regulation of plastids and mitochondria in three tissues representing carbon source (mature leaf), sink (immature xylem) and transport (secondary phloem) tissues. This research has improved our understanding of carbon allocation during xylogenesis, provided a resource for future studies in Eucalyptus organellar biology and is the first to look at the transcriptomes of secondary growth plastids and mitochondria. Important findings from this work include that the regulation of plastid and mitochondrial metabolism is highly integrated with xylem development and the circadian clock. Plastid specific associations with the central circadian clock and epigenetic regulation show that the central functions of plastid retrograde signalling in leaf and green vascular tissues are conserved in wood formation. Finally, analysis of organellar transcriptomes in multiple tissues has shown for the first time that nuclearencoded polymerases uniquely drive plastidial gene expression during wood formation and that (as yet unknown) nuclear-encoded RNA-binding proteins may be involved in the active upregulation of selected plastid-encoded genes to facilitate nonphotosynthetic metabolism in the plastids of tree sink tissues. In conclusion, the thesis makes an evidence-based argument for a specific plastid type – the xyloplast – to advance research in the field of wood formation and organellar biology.